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Yorodumi- PDB-2cdq: Crystal structure of Arabidopsis thaliana aspartate kinase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cdq | ||||||
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Title | Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine | ||||||
Components | ASPARTOKINASE | ||||||
Keywords | TRANSFERASE / ASPARTATE KINASE / AMINO ACID METABOLISM / ACT DOMAIN / ALLOSTERY / S-ADENOSYLMETHIONINE / LYSINE / ALLOSTERIC EFFECTOR / PLANT / AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / chloroplast stroma / amino acid biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Mas-Droux, C. / Curien, G. / Robert-Genthon, M. / Laurencin, M. / Ferrer, J.L. / Dumas, R. | ||||||
Citation | Journal: Plant Cell / Year: 2006 Title: A Novel Organization of Act Domains in Allosteric Enzymes Revealed by the Crystal Structure of Arabidopsis Aspartate Kinase Authors: Mas-Droux, C. / Curien, G. / Robert-Genthon, M. / Laurencin, M. / Ferrer, J.L. / Dumas, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdq.cif.gz | 193 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdq.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cdq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2cdq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2cdq_validation.xml.gz | 37 KB | Display | |
Data in CIF | 2cdq_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdq ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.00055, -1, 0.00014), Vector: |
-Components
#1: Protein | Mass: 55960.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LYU8, aspartate kinase #2: Chemical | ChemComp-LYS / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 74 % Description: THIS A. THALIANA AK STRUCTURE WAS OBTAIN BY MOLECULAR REPLACEMENT USING A FIRST AK MODEL AT 3.1 A RESOLUTION SOLVED USING MAD METHOD SELENOMETHIONINE SUBTITUTION |
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Crystal grow | pH: 6.5 Details: 0.2 M DI-SODIUM TARTRATE DIHYDRATE, 20 % PEG 3350, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. obs: 38693 / % possible obs: 96.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→15.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 27.077 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→15.67 Å
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Refine LS restraints |
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